The President is a civilian, and there is no protocal calling for a civilian to salute the military, just as there is no protocal for a civilian to salute the flag. In fact, the president saluting the military is implying that the military is not subserviant to civilian authority, which I find downright scary.
PLEASE obama, stop saluting the military from this day forward. PLEASE. ANYTHING that can be used to bash you with is a good thing, not a bad thing.